Scientists have trained mice to recognize the whiff of bird flu in duck poop, and they think they can train dogs to do the same thing. If so, flu-sniffing dogs — or chemical sensors built to duplicate this not-so-stupid pet trick — could become a new line of defense in the fight against epidemics.

The latest findings focus on the detection of avian influenza, a.k.a. bird flu. But Bruce Kimball, a U.S. Department of Agriculture researcher who presented the study today in Boston at a meeting of the American Chemical Society, suggested that the trick could be used to sniff out other diseases as well. “To be honest with you, I think we could demonstrate this type of effect in a lot of areas,” he told me.

You begin your book The Artificial Ape by claiming that Darwin was wrong. In what way?

Darwin is one of my heroes, but I believe he was wrong in seeing human evolution as a result of the same processes that account for other evolution in the biological world – especially when it comes to the size of our cranium.

Darwin had to put large cranial size down to sexual selection, arguing that women found brainy men sexy. But biomechanical factors make this untenable. I call this the smart biped paradox: once you are an upright ape, all natural selection pressures should be in favour of retaining a small cranium. That’s because walking upright means having a narrower pelvis, capping babies’ head size, and a shorter digestive tract, making it harder to support big, energy-hungry brains. Clearly our big brains did evolve, but I think Darwin had the wrong mechanism. I believe it was technology. We were never fully biological entities. We are and always have been artificial apes.

So you are saying that technology came before humans?

The archaeological record shows chipped stone tool technologies earlier than 2.5 million years ago. That’s the smoking gun. The oldest fossil specimen of the genus Homo is at most 2.2 million years old. That’s a gap of more than 300,000 years – more than the total length of time that Homo sapiens has been on the planet. This suggests that earlier hominins called australopithecines were responsible for the stone tools.

Is it possible that we just don’t have a genus Homo fossil, but they really were around?

Some researchers are holding out for an earlier specimen of genus Homo. I’m trying to free us to think that we had stone tools first and that those tools created a significant part of our intelligence. The tools caused the genus Homo to emerge.

My take: so what? Being a good athlete means that you are good at sports. That is fine; I enjoy boxing,NBA, NFL and track action. But being a good athlete hardly means being a hero. Scandals? Meh. Sure, I don’t like cheating. But this off the field/court/out of the ring stuff means little; these peoples are really a type of entertainer and not much else. Scandals involving our elected leaders or, say, scientists who falsify research bother me much more.

The opposition to science doesn’t seem to know any party bounds. On the right, global-warming skepticism is the rule, evolution a minority ‘opinion’, and if WorldNetDaily is to be believed, soy turns your kids gay.

On the left, we’ve now got the Huffington Post, recently lending their voice to Deepak Chopra, who in his latest contributions to the site expounded his philosophy of the mind (or whatever you want to call it), apparently seeking to justify it in quantum mechanics. Which gives it unwarranted legitimacy and worse, spreads disinformation about the science. Being somewhat qualified to rebut this, I thought I would try.

* BluePlatypus’s diary :: ::
*

Now it’s far from the first time the Huffington Post has gone off promoting bad science, pseudoscience or outright crankery, having for instance lent its voice to Jim Carrey (in his latest role as an immunologist) preaching the ‘dangers’ of vaccines. I’m not the only one around here who seems to think they’ve grown increasingly sensationalist as well as anti-science (although this is more in the realm of ‘bad science’). […]

This is the one quantum-mechanical property that’s relevant to this discussion, which is that in quantum mechanics, things can exist in several states at once. (called a superposition) Objects don’t have definite locations; rather they’re ‘smeared out’ over space. The lighter they are, and the faster they move, the more ‘smeared out’ they can be. (those who’ve read about QM before know I’m referring to the famous Uncertainty Principle)

But if a measurement is carried out on the object, it will have a certain value. Which is part of the ‘weirdness’. QM cannot predict what value will be measured, but it can predict the probability of all the possible measurement results. It can predict the average of a large number of measurements. For instance, the electron of a hydrogen atom is most likely to be 53 picometers away from the nucleus. But a single measurement could give any result from zero to infinity.

Heavier, bigger, things on the other hand, get less and less ‘smeared out’, and you end up with the ‘classical’ situation, where things assume definite values for their location and speed and other things.

Chopra (and many, many others) misinterprets what ‘measurement’ means here, assuming that it has something to do with human activity, drawing not only the erroneous conclusion that human (or sentient) perception is what’s meant by ‘measurement’, but indeed that things don’t even exist if they’re not being ‘measured’. Stating: “In fact, everything you are looking at right now depends upon you to exist.”

This is a basic misconception which has been debunked repeatedly (no doubt several times a week on physics newsgroups and message boards). Quantum mechanical measurements have nothing to do with ‘measurement’ per se, and especially not with human activity. It’s also at the basis of the Schrödinger’s cat ‘paradox’, as well as many of the early confusion about quantum mechanics.

In short, it’s a process known as decoherence. It’s not fully understood yet (although a lot of progress has been made since the early days and early confusion of QM). Decoherence is the process whereby quantum systems go from a superposition of different states to a single, definite state, through interactions with their environment. It’s ‘locked’ into this state because there’s an increase in entropy (disorder) associated with that change, making it irreversible (2nd law). It’s not fully understood yet, but it certainly doesn’t resemble the Berkleyian idea Chopra seems to have adopted.

This is an excellent article; if you like science and debunking quackery, read it!

Personal note: I am feeling weird; just “off”. My digestion is out of whack, I have some thigh aches (due to the stepper?) and am just “off” and tired. I am recording this so I can see if this leads to sickness or not. I am not feeling horrible; my workout this morning was slightly sub par but within standard variation.

We all get spam in our mail box and usually there’s nothing you can do about it. This time there is. I got this message today.

Subject: Award Acknowledgment for sharing great PHYSICS information to the public

Dear Blog Owner,

Our website Science.org is a informational databases and online news publication for anything and everything related to science and technology. We recently ran a poll asking our website users regarding what online informational resources they use to keep up to date or even to simply find great information. It seems many of our users have labeled your blog as an excellent source of Space information.

Note: his blog is about biochemistry and evolution. I had to chuckle.

Back when I was an undergraduate, I subscribed to Scientific American for a short while. Hence I got on some lists and I got an invitation to subscribe to some other science publication (I can’t remember which one). But I remember how the invitation started:

Dear Colleague,
We know of your work and….

And I thought: “they graded my advanced calculus homework?” 🙂 Remember that I was a run of the mill undergraduate pin-head at the time; I hadn’t done any individual research.

Last week the Vatican invited Anglicans who are, as The New York Times put it, “uncomfortable with female priests and openly gay bishops” to reunite with the Roman Catholic Church. If a secular institution, Wal-Mart or Microsoft, for example, made a similar offer — Tired of leadership positions being open to women and gay employees? Join us! — it would be slammed for appealing to bigotry. Some criticism was directed at the church, but it was faint. Are we right to speak softly when discussing a subject as sensitive as religion?

Etiquette holds that religion, especially another person’s religion, should be treated with deference or, better still, silence by nonbelievers. [….]

Yet despite the risk of provoking the ire of believers, we should discuss the actions of religious institutions as we would those of all others — courteously and vigorously. This is a mark of respect, an indication that we take such ideas seriously. To slip on the kid gloves is condescending, akin to the way you would treat children or the frail or cats.

[…] The week I rebuked an Orthodox Jewish real estate agent whose beliefs forbade his shaking the hand of a female client, I stopped counting after receiving 4,000 ferocious messages, lambasting not only my argument but my character, my appearance and my parentage: it was speculated that dogs played a part.

My political beliefs, my ideas about social justice, are as deeply held as my critics’ religious beliefs, but I don’t ask them to treat me with reverence, only civility. They should not expect me to walk on tiptoe.

Predictably, after the Ft. Hood shooting some idiot conservatives are suggesting that we do some sort of loyalty exam for Muslim-Americans before allowing them into the US military. Who is “we”? Who gets to do this exam? What, presumably more American people like whites or Christians?

Why don’t Muslim Americans decide which Christians get to enter the US military? Oh, does that sound offensive? Does it sound weird? Why should it sound any different than Christians getting to decide which other Americans they will allow into the US military?

* Cenk Uygur’s diary :: ::
*

A lot of people are rightfully making the point that you can not generalize about millions of Muslims in this country based on two guys. Just as you cannot generalize about all right-leaning white Christians (let alone all Christians in their entirety) based on what domestic terrorists like Tim McVeigh did, or Terry Nichols, or Eric Rudolph, or Scott Roeder or …

But there is a more important point here. Muslims Americans don’t have to prove a damn thing to you. They are Americans just like anyone else, whether right-wing clowns like it or not. They are not 80% American. They are not 90% as American as you are. You don’t get to judge how American they are.

Here is the inalterable fact that the right-wing of this country has to get used to – Muslim-Americans are 100% American. There are no degrees of how American you are. They have the same exact rights, privileges and responsibilities as any other American does. They don’t have to answer to you.

I’m agnostic now, but I was born Muslim. My whole family is Muslim. They’re all Americans. Not one of them is one percent less of an American than any other race or religion in this country.

“So what”, you say? Let me ask this: why is it that every time someone like Louis Farrakhan says something idiotic, some right wingers expect prominent African American leaders to denounce him? There were times when Americans of Mexican descent were supposed to denounce something stupid that the Mexican government did. Why is that?

In all honesty, if your skin isn’t white, you are always going to be viewed as a “guest”; perhaps an accepted guest or maybe a part of the adopted family. It is subtle, but it is there.

In the midst of a seriously disgusting interview with Dick Armey, the former House majority leader offers his analysis of the financial crisis:

But at what point do we allow the government to order people that you must sell your product to this person or that person, irrespective of any good judgment? We saw what happened in housing when they ordered banks to make loans to people who weren’t qualified. Are we now going to have the same destructive influences in health care because we’re going to order doctors to provide services and so forth?

There’s a persistent delusion, on the part of many pundits, to the effect that we’re actually having a rational political discussion in this country. But we aren’t. The proposition that the Community Reinvestment Act caused all the bad stuff, because government forced helpless bankers into lending to Those People, has been refuted up, down, and sideways. The vast bulk of subprime lending came from institutions not subject to the CRA. Commercial real estate lending, which was mainly lending to rich white developers, not you-know-who, is in much worse shape than subprime home lending. Etc., etc.

Workout notes Nothing yet; yoga class to come, then 6-7 miles of running, a couple of walking then getting my expired license plate tags renewed. I was a bonehead for not getting them renewed in time.

Other topics first

7 minute video: mathematical model of war and insurgency. One can actually predict (via a relatively simple stochastic function) the frequency and intensity of attacks from an insurgency; the predictor variable is the degree to which the insurgents are organized (on a scale from few, but tightly organized groups to more but less effective groups; the former situation shows more promise for negotiation; the latter may well signify that the insurgency is too weak to sustain itself)

Kemp’s good idea was that the Republicans should vastly expand their tent, get past their narrow-mindedness and begin actively seeking the support of blacks and other ethnic minorities.

The G.O.P. would have none of it. It was, after all, the party of the southern strategy, and there was precious little that was racially enlightened about its conservative wing. One of the writers who influenced Kemp’s thinking about politics, William F. Buckley, was at the opposite pole of Kemp’s progressive thinking about race. Buckley took a scurrilous stand in the aftermath of the Brown v. Board of Education decision that desegregated the nation’s public schools.

Whites, being superior, were well within their rights to discriminate against blacks, according to Buckley. “The White community is so entitled,” he wrote, “because, for the time being, it is the advanced race …”

Kemp was whistling in a hurricane.

He goes on to talk about Kemp’s bad ideas (economic). But at least Kemp cared about the disadvantaged; his solution was to aggressively pursue “economic zones” where investors would be encouraged to invest in poor minority areas, thereby bringing jobs and tax revenue to impoverished areas. The idea is NOT crazy; this is a case where I’d be willing to say “ok, let’s give this conservative idea a shot and see how it works”.

The current outbreak shows how complex and mysterious the evolution of viruses is. That complexity and mystery are all the more remarkable because a virus is life reduced to its essentials. A human influenza virus, for example, is a protein shell measuring about five-millionths of an inch across, with 10 genes inside. (We have about 20,000.)

Some viruses use DNA, like we do, to encode their genes. Others, like the influenza virus, use single-strand RNA. But viruses all have one thing in common, said Roland Wolkowicz, a molecular virologist at San Diego State University: they all reproduce by disintegrating and then reforming.

A human flu virus, for example, latches onto a cell in the lining of the nose or throat. It manipulates a receptor on the cell so that the cell engulfs it, whereupon the virus’s genes are released from its protein shell. The host cell begins making genes and proteins that spontaneously assemble into new viruses. “No other entity out there is able to do that,” Dr. Wolkowicz said. “To me, this is what defines a virus.” […]

Viruses are diverse because they can mutate very fast and can mix genes. They sometimes pick up genes from their hosts, and they can swap genes with other viruses. Some viruses, including flu viruses, carry out a kind of mixing known as reassortment. If two different flu viruses infect the same cell, the new copies of their genes get jumbled up as new viruses are assembled. […]

From time to time, a new kind of flu emerges that causes far more suffering than the typical swarm of seasonal flu viruses. In 1918, for example, the so-called Spanish flu caused an estimated 50 million deaths. In later years, some of the descendants of that strain picked up genes from bird flu viruses.

Sometimes reassortments led to new pandemics. It is possible that reassortment enables flu viruses to escape the immune system so well that they can make people sicker and spread faster to new hosts.

Reassortment also played a big role in the emergence of the current swine flu. Its genes come from several ancestors, which mainly infected pigs.

Scientists first isolated flu viruses from pigs in 1930, and their genetic sequence suggests that they descend from the Spanish flu of 1918. Once pigs picked up the flu from humans, that so-called classic strain was the only one found in pigs for decades. But in the 1970s a swine flu strain emerged in Europe that had some genes from a bird flu strain. A different pig-bird mix arose in the United States.

In the late 1990s, American scientists discovered a triple reassortant that mixed genes from classic swine flu with genes from bird viruses and human viruses. All three viruses — the triple reassortant, and the American and European pig-bird blends — contributed genes to the latest strain. […]

Fortunately, the new swine virus seems to behave like seasonal flu in terms of severity, not like the 1918 Spanish flu. “Right now it doesn’t have what it takes to be a killer virus,” Dr. Palese said. But could it? Dr. Palese said it was highly unlikely.

If the swine flu peters out in the next few weeks, virus trackers will still pay close attention to it over the next few months. As flu season ends in the Northern Hemisphere, the virus may be able to thrive in the southern winter or perhaps linger in the tropics, only to return to the north next fall. It will no doubt change along the way as its genes mutate, and it may pick up new genes.

As I noted below, it looks like Sen. Jeff Sessions (R-AL) will be, at least for a time, the ranking member on the Judiciary Committee. That’s an interesting role for a man with Sessions’…history. In a 2002 New Republic article, Sarah Wildman detailed the Alabama senator’s rise through the ranks of politics in Alabama and in Republican Washington.

Sessions first appeared on the scene in 1986 D.C. when President Ronald Reagan nominated him to serve on the U.S. District Court in Alabama. At the time, the Judiciary Committee was controlled by Republicans, but his appointment nonetheless went absolutely nowhere–a fact that may have had a thing or two to do with stories like this:

Senate Democrats tracked down a career Justice Department employee named J. Gerald Hebert, who testified, albeit reluctantly, that in a conversation between the two men Sessions had labeled the National Association for the Advancement of Colored People (NAACP) and the American Civil Liberties Union (ACLU ) “un-American” and “Communist-inspired.” Hebert said Sessions had claimed these groups “forced civil rights down the throats of people.” In his confirmation hearings, Sessions sealed his own fate by saying such groups could be construed as “un-American” when “they involve themselves in promoting un-American positions” in foreign policy. Hebert testified that the young lawyer tended to “pop off” on such topics regularly, noting that Sessions had called a white civil rights lawyer a “disgrace to his race” for litigating voting rights cases. Sessions acknowledged making many of the statements attributed to him but claimed that most of the time he had been joking, saying he was sometimes “loose with [his] tongue.” He further admitted to calling the Voting Rights Act of 1965 a “piece of intrusive legislation,” a phrase he stood behind even in his confirmation hearings….

Keep it up Republicans. I’m sure that this is probably ok for many of Senator Sessions constituents’. That attitude probably works in other southern regions as well. But more and more, the current Republicans are reminding me of the old South Africa’s pro-apartheid National Party. No, they aren’t nearly that bad, but they represent a past America and, while still popular in certain regions of the country, aren’t going to be a national party anytime soon.

I wonder if they will come up with someone who will lead them into the 21st century? My guess is “yes”, eventually.

So what about the rumors of President Obama’s nominee? Right now, no one outside of a tight circle really knows; here is one likely candidate. There are things that I like about her, and things that I don’t. If she is indeed being vetted, time will tell how it all shakes out. (hat tip to the Legal Satyricon for the last link). I recommend following the link because there is some interesting discussion on the legal merits of the decision that Judge Sotomayor signed onto. This snippet comes from here:

But she has one major, very bad decision on free speech and press to her discredit, which should give everyone who values these freedoms in our society serious cause for concern about Sotomayor’s possible nomination to the High Court.

The decision came from Sotomayor’s Second Circuit Court last May, regarding Lewis Mills High School student Avery Doninger. While running for Senior Class Secretary, Ms. Doninger found reason to object to the school’s cancellation of a “jamfest” event, and characterized those who scotched the event as “douchebags” on her off-campus LiveJournal blog (she also characterized a school official in that same blog posting as getting “pissed off”). The school officials, in turn, took umbrage, prohibited Avery from running for Class Secretary, and disregarded the plurality of votes she received, anyway, as a write-in candidate. Avery sued the school officials, and the Federal District Court supported the school. Avery appealed to Sotomayor’s Second Circuit Court.

After acknowledging the Supreme Court’s 1969 Tinker decision, which held that students do not “shed their constitutional rights to freedom of speech or expression at the schoolhouse gate,” Sotomayor’s Court proceeded to affirm the District Court’s ruling – that is, Sonia Sotomayor and her colleague justices upheld the high school’s right to punish Doninger for her off-campus speech. Their reasoning was that schools have an obligation to impart to their students “shared values,” which include not only the importance of free expression but a “proper respect for authority”.

Bill Maher nails it on evolution and the current strain of the Swine flu:

Science and the Cosmos

It is known (from quantum mechanics) that observation affects the state of a system; the state of a system has a “wave function” assigned to it and observation “collapses the wave function.” This is highly counter-intuitive.
Physicists have tried to come up with models to explain this, and one of them is the so-called biocentric model: this model supposes that life is what creates time, space and the cosmos! This article attempts to explain this school of thought:

Figuring out the nature of the real world has obsessed scientists and philosophers for millennia. Three hundred years ago, the Irish empiricist George Berkeley contributed a particularly prescient observation: The only thing we can perceive are our perceptions. In other words, consciousness is the matrix upon which the cosmos is apprehended. Color, sound, temperature, and the like exist only as perceptions in our head, not as absolute essences. In the broadest sense, we cannot be sure of an outside universe at all.

Ok, then why do different people come to the same conclusion?

SEEKING SPACE AND TIME
Even the most fundamental elements of physical reality, space and time, strongly support a biocentric basis for the cosmos.

According to biocentrism, time does not exist independently of the life that notices it. The reality of time has long been questioned by an odd alliance of philosophers and physicists. The former argue that the past exists only as ideas in the mind, which themselves are neuroelectrical events occurring strictly in the present moment. Physicists, for their part, note that all of their working models, from Isaac Newton’s laws through quantum mechanics, do not actually describe the nature of time. The real point is that no actual entity of time is needed, nor does it play a role in any of their equations. When they speak of time, they inevitably describe it in terms of change. But change is not the same thing as time.

To measure anything’s position precisely, at any given instant, is to lock in on one static frame of its motion, as in the frame of a film. Conversely, as soon as you observe a movement, you cannot isolate a frame, because motion is the summation of many frames. Sharpness in one parameter induces blurriness in the other. Imagine that you are watching a film of an archery tournament. An archer shoots and the arrow flies. The camera follows the arrow’s trajectory from the archer’s bow toward the target. Suddenly the projector stops on a single frame of a stilled arrow. You stare at the image of an arrow in midflight. The pause in the film enables you to know the position of the arrow with great accuracy, but you have lost all information about its momentum. In that frame it is going nowhere; its path and velocity are no longer known. Such fuzziness brings us back to Heisenberg’s uncertainty principle, which describes how measuring the location of a subatomic particle inherently blurs its momentum and vice versa.

All of this makes perfect sense from a biocentric perspective. Everything we perceive is actively and repeatedly being reconstructed inside our heads in an organized whirl of information. Time in this sense can be defined as the summation of spatial states occurring inside the mind. So what is real? If the next mental image is different from the last, then it is different, period. We can award that change with the word time, but that does not mean there is an actual invisible matrix in which changes occur. That is just our own way of making sense of things. We watch our loved ones age and die and assume that an external entity called time is responsible for the crime.

There is a peculiar intangibility to space, as well. We cannot pick it up and bring it to the laboratory. Like time, space is neither physical nor fundamentally real in our view. Rather, it is a mode of interpretation and understanding. It is part of an animal’s mental software that molds sensations into multidimensional objects.

In short, what we know of the universe is some sort of approximation that our brains are capable of making..or does our attempting to make sense of it make it what it is? What if there were other observant beings out there? How does their observation affect the cosmos, or how does it affect what we interpret as the cosmos? It looks as if my reading list got a bit longer. 🙂

As far as the David Brooks article: I still think that natural talent is real; I could think about things all day for years at a time and never become, say, a Terrance Tao. (Fields Medalist).

Side note: I am going to certainly use my recent teaching experience (linear algebra, abstract algebra, differential equations) as a springboard to finish up some mathematics articles and to read up on some (new to me) research techniques.

In a nutshell this is what happens: if public health organizations react quickly to keep the disease from spreading in the first place, the time to the peak of the disease (in terms of the number of people getting sick) is longer and the number of people getting sick at the peak is far lower:

And here is what happened in 1918 (Philadelphia, which took no preventative steps versus St. Louis, which did)

I fully welcome feedback from doctors, public health people, biologists, and those who know more.

About Blueollie

To keep track of my sports activities. I rarely train for anything anymore; mostly I just do workouts of the following types: running, walking, weight lifting and swimming. My best ultra accomplishment was walking 101 miles in 24 hours in 2004. These days, I walk a marathon every once in a while (5:50 to 7 hours) There was a time when I could run a sub 40 minute 10K (did that once), but that was another lifetime ago; these a days 2427-282525:50-27:45 28-31 minutes for a 5K would be more like it. I also have an off and on interest in yoga and in weight training. My lifetime PB in the bench is 310; currently I do sets of 4-5 with 190 185.

Best this year has been 200 (relatively easy).

To discuss the football, basketball or baseball game I’ve been to. Since 2011, I started to attend live football games regularly (University of Illinois, sometimes Illinois State, sometimes either the Colts or Bears of the NFL…don’t get me started on the Rams) ; I’ve attended Bradley Basketball games (men and women) for some time. In the past 3 years, I started to watch live baseball again (mostly the Peoria Chiefs (low A affiliate of the Cardinals) and Bradley University; sometimes the Normal Cornbelters (Frontier League; similar to low A level ball).

From time to time, I post what I am thinking about mathematically

I often post links to science articles, especially articles about cosmology and evolution.

I am very sympathetic to the “new atheist” movement, though some might consider me to be an agnostic. I reject any notion of a deity that interferes with physical events, but remain agnostic to the idea that there might be something “grand and wonderful” (Dawkins’ phrase) outside of our current spacetime continuum.

I am a liberal Democrat who thinks that the current social atmosphere is tilted way too far toward the interests of big business, and I reject the idea that a “free market” cures all ills, though pure socialism doesn’t work either. I am also a believer in the freedom of speech, including speech that I might not like. Also, I’ve been involved (to a moderate degree) with political campaigns, ranging from City Council races up to Presidential races.

I like to post photos of trips and vacations.

I like women in spandex. 🙂

The 2016 election: I voted for Hillary Clinton and was dismayed that she lost the Electoral College, though I take a bit of comfort that a plurality of voters preferred her (by just over 2 percentage points!)

I see Donald Trump as an unqualified amateur who lacks the humility and deportment to be an effective president; I sure hope the time proves me wrong. It does not appear that I am wrong though (as of June, 2018) I’ve been wrong before (e. g. my election prediction) and will be wrong again. I hope this is one of those times.